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Lmx1a LIM homeobox transcription factor 1 alpha [ Mus musculus (house mouse) ]

Gene ID: 110648, updated on 17-Nov-2020

Summary

Official Symbol
Lmx1aprovided by MGI
Official Full Name
LIM homeobox transcription factor 1 alphaprovided by MGI
Primary source
MGI:MGI:1888519
See related
Ensembl:ENSMUSG00000026686
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
dr; sst; Lmx1.; Lmx1.1; dreher
Expression
Biased expression in CNS E11.5 (RPKM 3.7), placenta adult (RPKM 2.2) and 8 other tissues See more
Orthologs

Genomic context

See Lmx1a in Genome Data Viewer
Location:
1 H2.3; 1 75.08 cM
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (167515799..167676310)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (167688230..167848741)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (169619689..169778864)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34207 Neighboring gene leucine rich repeat containing 52 Neighboring gene retinoid X receptor gamma Neighboring gene pre B cell leukemia homeobox 1 Neighboring gene predicted gene, 51671 Neighboring gene predicted gene, 39696

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC129356, MGC129357

Gene Ontology Provided by MGI

Process Evidence Code Pubs
axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
brain development ISO
Inferred from Sequence Orthology
more info
 
central nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
central nervous system neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cerebellum development IMP
Inferred from Mutant Phenotype
more info
PubMed 
dentate gyrus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
dopaminergic neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
hippocampus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
locomotory behavior IGI
Inferred from Genetic Interaction
more info
PubMed 
memory IGI
Inferred from Genetic Interaction
more info
PubMed 
midbrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
midbrain dopaminergic neuron differentiation IDA
Inferred from Direct Assay
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
olfactory behavior IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation IC
Inferred by Curator
more info
PubMed 
positive regulation of canonical Wnt signaling pathway IC
Inferred by Curator
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
synapse organization IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
LIM homeobox transcription factor 1-alpha
Names
LIM/homeobox protein 1.1
LIM/homeobox protein LMX1A
LMX-1.1
shaker short-tail

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_033652.5NP_387501.1  LIM homeobox transcription factor 1-alpha

    See identical proteins and their annotated locations for NP_387501.1

    Status: PROVISIONAL

    Source sequence(s)
    AC093452, AC160530
    Consensus CDS
    CCDS15460.1
    UniProtKB/Swiss-Prot
    Q9JKU8
    UniProtKB/TrEMBL
    Q543W2
    Related
    ENSMUSP00000028003.6, ENSMUST00000028003.8
    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198252
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    167515799..167676310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006496611.3XP_006496674.1  LIM homeobox transcription factor 1-alpha isoform X1

    See identical proteins and their annotated locations for XP_006496674.1

    UniProtKB/Swiss-Prot
    Q9JKU8
    UniProtKB/TrEMBL
    Q543W2
    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198252
    Homeobox; Homeobox domain
  2. XM_017321684.2XP_017177173.1  LIM homeobox transcription factor 1-alpha isoform X1

    UniProtKB/Swiss-Prot
    Q9JKU8
    UniProtKB/TrEMBL
    Q543W2
    Related
    ENSMUSP00000107008.1
    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198252
    Homeobox; Homeobox domain
  3. XM_030242132.2XP_030097992.1  LIM homeobox transcription factor 1-alpha isoform X1

    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198252
    Homeobox; Homeobox domain
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